posted on 2024-01-26, 10:29authored byKlemens Fröhlich, Regula Furrer, Christian Schori, Christoph Handschin, Alexander Schmidt
In recent years, a plethora of different data-independent
acquisition
methods have been developed for proteomics to cover a wide range of
requirements. Current deep proteome profiling methods rely on fractionations,
elaborate chromatography, and mass spectrometry setups or display
suboptimal quantitative precision. We set out to develop an easy-to-use
one shot DIA method that achieves high quantitative precision and
high proteome coverage. We achieve this by focusing on a small mass
range of 430–670 m/z using
small isolation windows without overlap. With this new method, we
were able to quantify >9200 protein groups in HEK lysates with
an
average coefficient of variance of 3.2%. To demonstrate the power
of our newly developed narrow mass range method, we applied it to
investigate the effect of PGC-1α knockout on the skeletal muscle
proteome in mice. Compared to a standard data-dependent acquisition
method, we could double proteome coverage and, most importantly, achieve
a significantly higher quantitative precision, as compared to a previously
proposed DIA method. We believe that our method will be especially
helpful in quantifying low abundant proteins in samples with a high
dynamic range. All raw and result files are available at massive.ucsd.edu
(MSV000092186).